The bay you sail shapes your trip more than the vessel you sail it on.
Most travellers pick a boat first and discover the route afterwards. We would suggest the reverse. The bay you sail decides your scenery, how many other vessels you see, which caves and beaches you visit, and even which harbour you drive to from Hanoi.
There are three cruising areas plus the island base of Cat Ba. They sit side by side and share the same limestone geology, but they feel noticeably different on the water.
Limestone islands and hidden lagoons across Halong Bay
The three bays, briefly
Halong Bay — the postcard route, with Sung Sot Cave and Titop Island, and the most boats
Lan Ha Bay — the same geology, greener islands, a fraction of the traffic
Bai Tu Long Bay — the quietest water and the longest transfer from Hanoi
Cat Ba Island — a base rather than a bay, good for trekking and cycling alongside the water
What genuinely changes between them
Scenery quality is broadly comparable — this is one continuous limestone landscape and none of the bays disappoints. What varies is boat density, which specific caves and beaches you reach, transfer length, and price.
Halong has the most vessels, which means the widest choice at every budget. Bai Tu Long has the fewest licensed operators, so options are narrower and prices firmer. Lan Ha sits between the two.
Our short recommendation
First visit and you want the famous scenery: Halong Bay, on a boat that departs early. Second visit, or you have seen the photographs and want peace: Lan Ha. Solitude above all: Bai Tu Long, ideally for two nights.
Tell us how you feel about crowds and how many nights you have. That answers the question faster than any comparison table.